Background: Heart failure is not a clear-cut diagnosis but a complex clinical syndrome with consequent diagnostic uncertainty. Judgment analysis is a method to help clinical teams to understand how they make complex decisions. The method of judgment analysis was used to determine the factors that influence clinicians' diagnostic decisions about heart failure. Methods: Three consultants, three middle grade doctors, and two junior doctors each evaluated 45 patient scenarios. The main outcomes were: clinicians' decisions whether or not to make a diagnosis of suspected heart failure; the relative importance of key factors within and between clinician groups in making these decisions, and the acceptability of the scenarios. Results: The method was able to discriminate between important and unimportant factors in clinicians' diagnostic decisions. Junior and consultant physicians tended to use patient information similarly, although junior doctors placed particular weight on the chest X-Ray. Middle-grade doctors tended to use information differently but their diagnostic decisions agreed with consultants more frequently (k = 0.47) than junior doctors and consultants (k = 0.23), or middle grade and junior grade doctors (k = 0.10). Conclusions: Judgment analysis is a potentially valuable method to assess influences upon diagnostic decisions, helping clinicians to manage the quality assurance process through evaluation of care and continuing professional development.